Genetic manipulation of isoflavonoids

ABSTRACT

Soybean and  Medicago truncatula  CYP93C genes have been isolated which encode a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone. Plants can now be genetically engineered to produce isoflavones that provide potential human health benefits and increase disease resistance in plants. Isoflavones can now be produced in transgenic plants species in which isoflavones do not naturally occur, i.e., in species other than legumes. Alternatively, introducing infection-inducible isoflavonoid biosynthesis into non-legumes qualitatively complements these plants phytoalexin defenses against microbial pathogens, whereas over-expression of the isoflavonoid pathway in legumes quantitatively increases this defense response. Finally, modifying the extend of production of isoflavonoids in legume roots positively impacts nodulation efficiency and therefore plant yield.

PRIORITY INFORMATION

This application is a §371 filing of International Application No. PCT/US00/05915, filed on Mar. 8, 2000, which claims benefit of Provisional Application No. 60/123,267, filed Mar. 8, 1999.

TECHNICAL FIELD OF THE INVENTION

The invention relates to gene manipulation in plants.

BACKGROUND OF THE INVENTION

The flavonoids are a major class of phenylpropanoid-derived plant natural products. Their fifteen carbon (C₆–C₃–C₆) backbone can be arranged as a 1,3-diphenylpropane skeleton (flavonoid nucleus) or as a 1,2-diphenylpropane skeleton (isoflavonoid nucleus). Although 1,3-diphenylpropane flavonoid derivatives are almost ubiquitous among terrestrial plants, the 1,2-diphenylpropane isoflavonoids are restricted primarily to the Leguminosae, although they occur rarely in other families such as the Apocynaceae, Pinaceae, Compositae, and Moraceae (Tahara, S. and R. K. Ibrahim, 1995, “Prenylated isoflavonoids—an update,” Phytochemistry 38: 1073–1094).

The limited taxonomic distribution of the isoflavonoids is directly related to the occurrence of the enzyme complex isoflavone synthase (IFS), which catalyzes the aryl migration reaction leading to the formation of an isoflavone from a flavanone. While flavanones are ubiquitous in higher plants, the IFS reaction, which is a two-step process specific for isoflavonoid biosynthesis (Kochs, G. and H. Grisebach, 1986, “Enzymic synthesis of isoflavones,” European J Biochem 155: 311–318), is limited to the Leguminosae and the other diverse taxa in which isoflavonoids are occasionally found.

The presence of isoflavonoids provides several advantages to plants. One such advantage is provided by the function of isoflavonoids as antimicrobial phytoalexins in plant-microbe interactions. For example, the simple isoflavones daidzein and genistein act as initial precursors in the biosynthesis of various antimicrobial isoflavonoid phytoalexins in a wide variety of legumes (Dixon, R. A. and N. L. Paiva, 1995, “Stress-induced phenylpropanoid metabolism,” Plant Cell 7: 1085–1097). Isoflavonoid compounds have been shown to accumulate in infected plant cells to levels known to be antimicrobial in vitro. The temporal, spatial and quantitative aspects of accumulation are consistent with a role for these compounds in disease resistance (Rahe, J. E., 1973, “Occurrence and levels of the phytoalexin phaseollin in relation to delimitation at sites of infection of Phaseolus vulgaris by Colletotrichum lindemuthianum,” Canadian J Botany 51: 2423–2430; Hadwiger, L. A. and D. M. Webster, 1984, “Phytoalexin production in five cultivars of pea differentially resistant to three races of Pseudomonas syringae pv. pisi,” Phytopathology 74: 1312–1314; Long, et al., 1985, “Further studies on the relationship between glyceollin accumulation and the resistance of soybean leaves to Pseudomonas syringae pv. glycinea,” Phytopathology 75: 235–239; Bhattacharyya, M. K. and E. W. B. Ward, 1987, “Biosynthesis and metabolism of glyceollin I in soybean hypocotyls following wounding or inoculation with Phylophihora megasperma f. sp. glycinea,” Physiol and Mol Plant Pathology 31: 387–405). Moreover, it has been reported that many plant pathogens are much more sensitive to phytoalexins of non-host species than they are to the phytoalexins of their natural hosts, because they can often detoxify the host's phytoalexins. (VanEtten, et al., 1989, “Phytoalexin detoxification: importance for pathogenicity and practical implications,” An Rev Phytopathology 27: 143–164).

Isoflavonoids also function in plant-microbe interactions in the establishment of bacterial or fungal symbioses with plants. Isoflavonoids have been reported to regulate bacterial nodulation genes, acting as a major nod gene inducer (Kosslak, et al., 1987, “Induction of Bradyrhizobium japonicum common nod genes by isoflavones isolated from Glycine max,” Proc Natl Acad Sci USA 84: 7428–7432) and/or transcription activator (Dakora, et al., 1993, “Common bean root exudates contain elevated levels of daidzein and coumestrol in response to Rhizobium inoculation,” Mol Plant-Microbe Interact 6: 665–668). Isoflavonoids have also been shown to have a role on the establishment of the symbiotic vesicular arbuscular mycorrhizal (VAM) association of the fungus Glomus with legume roots. (Kape, et al., 1992, “Legume root metabolites and VA-mycorrhiza development,” J Plant Physiol 141: 54–60). Xie et al have reported that the isoflavonoids coumestrol, daidzein and genistein have small but significant stimulatory effects on the degree of mycorrhizal colonization of soybean, and that one effect of isoflavonoids on the soybean mycorrhizal symbiosis could be via induction of nodulation factors from co-colonizing Rhizobia, since nod-factors have also been shown to stimulate fungal colonization (Xie, et al., 1995, “Rhizobial nodulation factors stimulate mycorrhizal colonization of nodulating and nonnodulating soybeans,” Plant Physiology 108: 1519–1525).

In addition to the advantages that the presence of isoflavonoids confers to plants, a significant body of evidence indicates that dietary consumption of isoflavonoids can provide benefits to human health. Dietary isoflavones have been ascribed strong cancer chemopreventative activity in humans, and display a range of pharmacological activities suggestive of various other health promoting effects, including phytoestrogen activity as both estrogenic and anti-estrogenic agents (Coward, et al., 1993, “Genistein, daidzein, and their -glycoside conjugates: antitumor isoflavones in soybean foods from American and Asian diets,” J Agricultural and Food Chemistry 41: 1961–1967; Martin, et al., 1996, “Interactions between phytoestrogens and human sex steroid binding protein,” Life Sciences 58: 429–436); anticancer effects associated with phytoestrogenic activity (Lee, et al., 1991, “Dietary effects on breast-cancer risk in Singapore,” Lancet 337: 1197–1200; Adlercreutz, et al., 1991, “Urinary excretion of lignans and isoflavonoid phytoestrogens in Japanese men and women consuming a traditional Japanese diet,” Am J Clin Nutr 54: 1093–1100); anticancer effects associated with inhibition of several enzymes including DNA topoisomerase and tyrosine protein kinase (Akiyama, et al., 1987, “Genistein, a specific inhibitor of tyrosine-specific protein kinases,” J Biol Chem 262: 5592–559; Uckun, et al., 1995, “Biotherapy of B-cell precursor leukemia by targeting genistein to CD19-associated tyrosine kinases,” Science 267: 886–891); suppression of alcohol consumption (Keung, W. M. and B. L. Vallee, 1993, “Daidzin: A potent, selective inhibitor of human mitochondrial aldehyde dehydrogenase,” Proc Natl Acad Sci USA 90: 1247–1251; Keung, et al., 1995, “Daidzin suppresses ethanol consumption by Syrian golden hamsters without blocking acetaldehyde metabolism,” Proc Natl Acad Sci USA 92: 8990–8993); antioxidant activity (Arora, et al., 1998, “Antioxidant activities of isoflavones and their biological metabolites in a lipsomal system,” Arch Biochem Biophys 356: 133–141; Tikkanen, et al., 1998, “Effect of soybean phytoestrogen intake on low density lipoprotein oxidation resistance,” Proc Natl Acad Sci USA 95: 3106–3110); effects on calcium metabolism, some of which may be linked to protective effects against osteoporosis (Tomonaga, et al., 1992, “Isoflavonoids, genistein, PSI-tectorigenin, and orobol, increase cytoplasmic free calcium in isolated rat hepatocytes,” Biochem Biophys Res Com 182: 894–899; Draper, et al., 1997, “Phytoestrogens reduce bone loss and bone resorption in oophorectomized rats,” J Nutr 127: 1795–1799); and cardiovascular effects (Wagner, et al., 1997, “Dietary soy protein and estrogen replacement therapy improve cardiovascular risk factors and decrease aortic cholesteryl ester content in ovariectomized cynomolgus monkeys,” Metabolism—Clinical and Experimental 46: 698–705).

At present, the only dietary sources of isoflavonoids for humans are certain legumes such as soybean or chickpea. The development of methods to genetically manipulate isoflavonoids in plants, either to widen the source of dietary isoflavonoids for humans, or to exploit the biological activities of isoflavonoids for plant protection and improvement, is wholly dependent on the availability of cloned genes encoding the various enzymes of isoflavonoid biosynthesis. Of these, the isoflavone synthase (IFS) complex constitutes the first committed reactions, and as such represents the means to introduce isoflavonoids into plants that do not possess the pathway.

In 1984, Hagmann and Grisebach provided the first evidence for the enzymatic conversion of flavanone to isoflavone (the IFS reaction) in a cell free system (Hagmann, M. and H. Grisebach, 1984, “Enzymatic rearrangement of flavanone to isoflavone,” FEBS Letters 175: 199–202). They demonstrated that microsomes from elicitor-treated soybean cell suspension cultures could catalyze the conversion of 2(S)-naringenin to genistein, or of 2(S)-liquiritigenin to daidzein, in the presence of NADPH. The crude microsomal enzyme preparation, which was stable at −70° C. but had a half-life of only 10 minutes at room temperature, was absolutely dependent on NADPH and molecular oxygen. It was subsequently shown that the reaction proceeded in two steps. The flavanone was converted in a cytochrome P450-catalyzed reaction requiring NADPH and O₂ to the corresponding 2-hydroxyisoflavanone. This relatively unstable compound, which could, however, be identified by mass spectrometric analysis, then underwent dehydration to yield the isoflavone. The dehydration reaction appeared to be catalyzed by an enzyme present predominantly in the cytoplasmic supernatant, although it was not possible to remove all this activity from the microsomes. The corresponding 2-hydroxyisoflavanone spontaneously converted to genistein, for example, in methanol at room temperature. Kinetic analysis indicated that the 2-hydroxyisoflavanone was formed prior to genistein, consistent with its being an intermediate in isoflavone formation. (Kochs, G. and H. Grisebach, 1986, “Enzymic synthesis of isoflavones,” European J Biochem 155: 311–318).

Involvement of cytochrome P450 in the 2-hydroxyisoflavanone synthase reaction was confirmed by inhibition by CO, replacing O₂ with N₂, and examining the effects of a range of known P450 inhibitors of which ancymidol was the most effective. The enzyme co-migrated with the endoplasmic reticulum markers cinnamate 4-hydroxylase (another cytochrome P450) and cytochrome b5 reductase on Percoll gradients. The enzyme is stereoselective, and (2R)-naringenin is not a substrate. (Kochs, G. and H. Grisebach, 1986, “Enzymic synthesis of isoflavones,” European J Biochem 155: 311–318).

The origin of the 2-hydroxyl group was determined from studies on the IFS present in microsomes from elicited cell cultures of Pueraria lobata. ¹⁸O from ¹⁸O₂ was incorporated into the 2-hydroxyl group, resulting in a 2-hydroxyisoflavanone with molecular ion shifted by two mass units, whereas there was no corresponding shift in the molecular ion of daidzein, consistent with the subsequent dehydration reaction (Hashim, et al., 1990, “Reaction mechanism of oxidative rearrangement of flavanone in isoflavone biosynthesis,” FEBS Letters 271: 219–222). The currently accepted model for the reaction pathway of IFS as illustrated in FIG. 1, therefore, involves P450-catalyzed hydroxylation coupled to aryl migration, a reaction with mechanistic similarities to the well described proton migration mechanism of some P450 reactions (Hakamatsuka, et al., 1991, “P450-dependent oxidative rearrangement in isoflavone biosynthesis: reconstitution of P-450 and NADPH:P450 reductase,” Tetrahedron 47: 5969–5978).

Currently, there have been no reports on purification to homogeneity or molecular cloning of the cytochrome P450 of the IFS complex because of the extreme lability of the enzyme. The 2-hydroxyisoflavanone synthase cytochrome P450 from Pueraria has been solubilized with Triton X-100, and partially purified by DEAE-Sepharose chromatography; the enzymatic reaction could be reconstituted by addition of NADPH cytochrome P450 reductase that separated from the hydroxylase on the ion exchange column (Hakamatsuka, et al., 1991, Tetrahedron 47: 5969–5978). A 2-hydroxyisoflavanone dehydratase has been purified from elicitor-treated P. lobata cells, and has been shown to be a soluble monomeric enzyme of subunit Mr 38,000 (Hakamatsuka, et al., 1998, “Purification of 2-hydroxyisoflavanone dehydratase from the cell cultures of Pueraria lobata,” Phytochemistry 49: 497–505). It is not yet clear whether this enzyme physically associates with the P450 hydroxylase catalyzing the aryl migration, or even whether this activity is essential for isoflavone formation in planta in view of the spontaneous conversion of 2-hydroxyisoflavanone to isoflavone.

Flavanone is a potential substrate for more than one type of hydroxylation reaction at the 2-position. Thus, elicitor-treated cell cultures of alfalfa and Glycyrrhiza echinata have been shown to accumulate the dibenzoylmethane licodione (Kirikae, et al., 1993, “Biosynthesis of a dibenzoylmethane, licodione, in cultured alfalfa cells induced by yeast extract,” Biosci Biotech Biochem 57: 1353–1354). Licodione synthase is, by classical criteria, a cytochrome P450, the activity of which is induced by yeast elicitor in Glycyrrhiza cells (Otani, et al., 1994, “Licodione synthase, a cytochrome P450 monooxygenase catalyzing 2-hydroxylation of 5-deoxyflavanone, in cultured Glycyrrhiza echinata L. cells,” Plant Physiol 105: 1427–1432). The reaction it catalyzes involves 2-hydroxylation of flavanone followed by hemiacetal opening instead of aryl migration, and the reaction was thought to have mechanistic similarities to the flavone synthase II enzyme previously characterized from soybean (Kochs, G. and H. Grisebach, 1987, “Induction and characterization of a NADPH-dependent flavone synthase from cell cultures of soybean,” Z. Naturforsch 42C: 343–348). A gene encoding the flavone synthase II/licodione synthase from Glycyrrhiza has been cloned (Akashi, et al., 1998, “Identification of a cytochrome P450 cDNA encoding (2S)-flavanone 2-hydroxylase of licorice (Glycyrrhiza echinata L.; Fabaceae) which represents licodione synthase and flavone synthase II,” FEBS Letters 431: 287–290), and a different cytochrome P450 gene encoding flavone synthase II has recently been cloned from Gerbera hybrida (Martens, S. and G. Forkmann, “Cloning and expression of flavone synthase II from Gerbera hybrids,” Plant J 20: 611–618).

Although the reactions catalyzed by IFS are critical for the formation of all isoflavonoids in plants, there have been no previous reports of the isolation of genes encoding components of isoflavone synthase, although genes encoding most of the other enzymes of the isoflavonoid pathway, including downstream enzymes converting simple isoflavones to antimicrobial phytoalexins, have been characterized (Dixon, et al., 1995, “The isoflavonoid phytoalexin pathway: from enzymes to genes to transcription factors,” Physiologia Plantarum 93: 385–392). Thus, the unavailability of isoflavone synthase genes has made it heretofore impossible to utilize the downstream genes for regulating isoflavonoid concentrations in legumes and other plants that do have the isoflavonoid pathway, or for engineering antimicrobial and pharmacologically active isoflavonoids in transgenic plants of species that do not have the isoflavonoid pathway.

Genes encoding the enzyme catalyzing the first step of the isoflavone synthase reaction have now been isolated and purified from soybean and Medicago truncatula (barrel medic).

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts the currently accepted model for the reaction pathway of IFS wherein the flavanone is converted in a cytochrome P450-catalyzed reaction requiring NADPH and O₂ to the corresponding 2-hydroxyisoflavanone which then undergoes dehydration to yield the isoflavone.

FIG. 2 depicts the nucleotide sequence of soybean CYP93C1v2(SEQ ID NO:1).

FIG. 3 depicts the amino acid sequence of soybean CYP93v2 (SEQ ID NO:2) compared to licorice CYP93B1 (SEQ ID NO:3).

FIG. 4 depicts the nucleotide sequence of Medicago truncatula mtIFSE3 (SEQ ID NO:4).

FIG. 5 depicts the amino acid sequence of Medicago truncatula mtIFSE3 (SEQ ID NO:5) compared to soybean CYP93C1v2 (SEQ ID NO:2).

FIG. 6A and FIG. 6B depict HPLC traces of extracts from pooled tissues (leaves, shoots, flowers) of Arabidopsis thaliana ecotype Columbia harboring an empty tDNA vector (FIG. 6A) and Arabidopsis thaliana ecotype Columbia harboring the soybean CYP93C1v2 cDNA sequence (FIG. 6B). The empty vector transformed line contains a number of flavonol glycosides and other phenolic compounds that are also present in the CYP93C1v2 transformed line. These compounds were identified as (a) rhamnose (Rha)-glucose (Glc)-quercetin (O), (b) uncharacterized conjugate of Q, (c) Rha-Glc-Rha-Kaempferol (K), (d) Glu-Rha-Q, (e) Rha—Rha-Q, (f) Glc-Rha-K, (g) sinapic acid, (h) Rha—Rha-K. Three additional compounds were observed in the CYP93C1v2 transformed line (FIG. 6B), and labeled “1,” “2” and “3.” FIG. 6C depicts a total ion chromatogram of partially purified peaks 2 and 3, and the insets show the specific ions generated from these compounds. Peak 2 has a parental molecular mass ion of 579.5 consistent with genistein conjugated to a glucose-rhamnose disaccharide, and two further mass ions of 417.5 and 271.3, representing Rha-genistein and free genistein, respectively. Peak 3, which has a parental molecular ion of mass 417.5, is thereby identified as Rha-genistein.

FIG. 7A and FIG. 7B depict HPLC traces of the same extracts as shown in FIG. 6A (empty-vector transformed) and FIG. 6B, (CYP93C1v2 transformed), but following digestion with α-glucosidase. Peaks 2 and 3 remained at the same retention time as in FIGS. 6A and 6B. However, Peak 1 disappeared, and was replaced with a new Peak 4 of much later retention time. FIG. 7C shows the total ion chromatograph of purified Peak 4, and the inset shows the parental molecular ion, with mass of 271.2, consistent with Peak 4 being free genistein. FIG. 7D shows a total ion chromatograph, and the parental molecular ion, of an authentic sample of genistein.

FIGS. 8A, 8B, 8C and 8D are high performance liquid chromatography (HPLC) chromatograms depicting the presence of new peaks at RT 29.96 and 37.7 min representing the presence of the isoflavone daidzein formed from the flavanone liquiritigenin, or the isoflavone genistein formed from the flavanone naringenin, in insect cell microsomes expressing CYP93C1v2. FIG. 8A depicts the presence of NADPH during incubation with liquiritigenin. FIG. 8B depicts the absence of NADPH during incubation with liquiritigenin. FIG. 8C depicts the presence of NADPH during incubation with naringenin. FIG. 8D depicts the lack of a reaction when soybean CYP93E expressed in insect cells is incubated with liquiritigenin in the presence of NADPH.

FIG. 9A and FIG. 9B are mass spectra of BSTFA (N,O-bis(trimethylsilyl) trifluoroacetamide) derivatives. FIG. 9A depicts the mass spectrum of the BSTFA derivative of the product of the reaction catalyzed by CYP93C1v2 in insect cells using liquiritigenin as substrate, and FIG. 9B shows the mass spectrum of the BSTFA derivative of an authentic sample of daidzein.

SUMMARY OF THE INVENTION

In one aspect, the invention is a method for introducing into a naturally non-isoflavonoid-producing plant species the enzyme catalyzing the aryl migration of a flavanone to form an isoflavanone intermediate or an isoflavone, comprising introducing a DNA segment encoding the enzyme into the plant to form a transgenic plant, wherein the transgenic plant expresses the DNA segment under the control of a suitable constitutive or inducible promoter when the transgenic plant is exposed to conditions which permit expression. The DNA segment can comprise isolated genomic DNA or recombinant DNA. Preferably, the DNA segment is a CYP93C gene. An exemplary DNA segment from a soybean CYP93C gene consists essentially of the sequence from about nucleotide 36 to about nucleotide 1598 of the sequence depicted in SEQ ID NO:1. Another preferred DNA segment comprises a Medicago truncatula homolog of a CYP93C gene, more preferably, the sequence from about nucleotide 92 to about nucleotide 1657 of the sequence depicted in SEQ ID NO:4. Plants transformed by this method may also preferably express chalcone synthase, chalcone reductase, and chalcone isomerase genes to cause in vivo formation of daidzein or a daidzein derivative, and the chalcone synthase, chalcone reductase, and chalcone isomerase genes may also be transgenes. Plants transformed by this method may also preferably further comprise downstream genes, for example, isoflavone O-methyltransferase, isoflavone 2′-hydroxylase, isoflavone reductase, and vestitone reductase, to metabolize a formed isoflavone to biologically active isoflavonoid derivatives or conjugates. The plant can comprise isoflavone 4′-O-methyl-transferase to cause formation of biochanin A or a biochanin A derivative from the isoflavanone intermediate. An exemplary flavanone substrate for this transformation method is liquiritigenin and/or naringenin.

In another aspect, the present invention is a method for increasing the level of isoflavonoid compounds in naturally isoflavonoid-producing plants comprising introducing a DNA segment encoding the enzyme catalyzing the aryl migration of a flavanone to yield an isoflavonoid to form a transgenic plant, wherein the transgenic plant expresses the DNA segment under the control of a suitable constitutive or inducible promoter when the transgenic plant is exposed to conditions which permit expression. With this method, the resulting isoflavonoid can be an isoflavanone intermediate, an isoflavone, an isoflavone derivative, and an isoflavone conjugate. The DNA segment can comprise isolated genomic DNA or recombinant DNA. Preferably, the DNA segment is a CYP93C gene. An exemplary DNA segment from a soybean CYP93C gene consists essentially of the sequence from about nucleotide 36 to about nucleotide 1598 of the sequence depicted in SEQ ID NO:1. Another preferred DNA segment comprises a Medicago truncatula homolog of a CYP93C gene, more preferably, the sequence from about nucleotide 92 to about nucleotide 1657 of the sequence depicted in SEQ ID NO:4. An exemplary flavanone substrate for this transformation method is liquiritigenin and/or naringenin.

In another aspect, the invention is a method for synthesizing an isoflavanone intermediate or an isoflavone from a flavanone by expressing a recombinant CYP93C gene segment in a suitable bacterial, fungal, algal, or insect cell system. An exemplary gene segment consists essentially of the sequence from about nucleotide 36 to about nucleotide 1598 of the sequence depicted in SEQ ID NO:1. Another exemplary gene segment consists essentially of the sequence from about nucleotide 92 to about nucleotide 1657 of the sequence depicted in SEQ ID NO:4.

In another aspect, the invention is a method of reducing the levels of isoflavonoid compounds in a naturally isoflavonoid-producing plant comprising introducing and expressing an antisense or gene silencing construct that contains an intact CYP93C gene or segments thereof into the plant. An exemplary gene consists essentially of the sequence from about nucleotide 36 to about nucleotide 1598 of the sequence depicted in SEQ ID NO:1. Another exemplary gene consists essentially of the sequence from about nucleotide 92 to about nucleotide 1657 of the sequence depicted in SEQ ID NO:4.

In another aspect, the invention is a naturally non-isoflavonoid-producing plant cell transformed by introducing a DNA segment encoding the enzyme catalyzing the aryl migration of a flavanone to form an isoflavanone intermediate or an isoflavone, wherein the transformed plant cell expresses the DNA segment under the control of a suitable constitutive or inducible promoter when exposed to conditions which permit expression. The DNA segment can comprise isolated genomic DNA or recombinant DNA. Preferably, the DNA segment is a CYP93C gene. An exemplary DNA segment from a soybean CYP93C gene consists essentially of the sequence from about nucleotide 36 to about nucleotide 1598 of the sequence depicted in SEQ ID NO:1. Another preferred DNA segment comprises a Medicago truncatula homolog of a CYP93C gene, more preferably, the sequence from about nucleotide 92 to about nucleotide 1657 of the sequence depicted in SEQ ID NO:4. Plants transformed by this method may also preferably express chalcone synthase, chalcone reductase, and chalcone isomerase genes to cause in vivo formation of daidzein or a daidzein derivative, and the chalcone synthase, chalcone reductase, and chalcone isomerase genes may also be transgenes. Plants transformed by this method may also preferably further comprise downstream genes, for example, isoflavone O-methyltransferase, isoflavone 2′-hydroxylase, isoflavone reductase, and vestitone reductase, to metabolize a formed isoflavanone intermediate to biologically active isoflavonoid derivatives or conjugates. The plant can comprise isoflavone 4′-O-methyl-transferase to cause formation of biochanin A or a biochanin A derivative from the isoflavanone intermediate.

In another aspect, the invention is a naturally isoflavonoid-producing plant cell transformed by introducing a DNA segment encoding the enzyme catalyzing the aryl migration of a flavanone to yield an isoflavonoid to form a transformed plant cell, wherein the transformed plant cell expresses the DNA segment under the control of a suitable constitutive or inducible promoter when exposed to conditions which permit expression. With this method, the resulting isoflavonoid can be an isoflavanone intermediate, an isoflavone, an isoflavone derivative, and an isoflavone conjugate. The DNA segment can comprise isolated genomic DNA or recombinant DNA. Preferably, the DNA segment is a CYP93C gene. An exemplary DNA segment from a soybean CYP93C gene consists essentially of the sequence from about nucleotide 36 to about nucleotide 1598 of the sequence depicted in SEQ ID NO:1. Another preferred DNA segment comprises a Medicago truncatula homolog of a CYP93C gene, more preferably, the sequence from about nucleotide 92 to about nucleotide 1657 of the sequence depicted in SEQ ID NO:4.

In another aspect, the invention is a transgenic plant cell having reduced levels of isoflavonoid compounds, the plant cell transformed by introducing an antisense or gene silencing construct that contains an intact CYP93C gene or segments thereof into the plant cell. An exemplary gene consists essentially of the sequence from about nucleotide 36 to about nucleotide 1598 of the sequence depicted in SEQ ID NO:1. Another exemplary gene consists essentially of the sequence from about nucleotide 92 to about nucleotide 1657 of the sequence depicted in SEQ ID NO:4.

In another aspect, the invention is an isolated gene or DNA segment comprising a portion which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the portion consists essentially of about nucleotide 36 to about nucleotide 1598 of the sequence depicted in SEQ ID NO:1. An exemplary gene is the soybean gene encoding the enzyme catalyzing the aryl migration of liquiritigenin. Another exemplary gene is the soybean gene encoding the enzyme catalyzing the aryl migration of naringenin.

In another aspect, the invention is a protein encoded by a portion of an isolated gene or DNA segment which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the portion consists essentially of about nucleotide 36 to about nucleotide 1598 of the sequence depicted in SEQ ID NO:1.

In another aspect, the invention is an isolated gene or DNA segment comprising a portion which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the portion is a Medicago truncatula homolog of a CYP93C gene. An exemplary gene or DNA segment consists essentially of about nucleotide 92 to about nucleotide 1657 of the sequence depicted in SEQ ID NO:4. An exemplary gene is the Medicago truncatula gene encoding the enzyme catalyzing the aryl migration of liquiritigenin. Another exemplary gene is the Medicago truncatula gene encoding the enzyme catalyzing the aryl migration of naringenin.

In another aspect, the invention is a protein encoded by a portion of an isolated gene or a DNA segment which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the portion is a Medicago truncatula homolog of a CYP93C gene.

In yet another aspect, the invention is a food comprising edible transgenic plant material capable of being ingested for its nutritional value, wherein the transgenic plant has been transformed with an isolated gene or DNA segment which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, and wherein the transgenic plant exhibits increased levels of an isoflavonoid when compared to the level of the isoflavonoid in plants of the same species which do not comprise the isolated gene or DNA segment.

In yet another aspect, the invention is a food comprising at least one isoflavonoid, wherein the isoflavonoid is isolated from a transgenic plant transformed with an isolated gene or DNA segment which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, and wherein the transgenic plant exhibits increased levels of an isoflavonoid when compared to the level of the isoflavonoid in plants of the same species which do not comprise the isolated gene or DNA segment.

In yet another aspect, the invention is a composition comprising at least a portion of a transgenic plant transformed with an isolated gene or DNA segment which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the transgenic plant exhibits increased levels of an isoflavonoid when compared to the level of the isoflavonoid in plants of the same species which do not comprise the isolated gene or DNA segment, and wherein the composition is suitable for ingestion as a food stuff, a nutritional supplement, an animal feed supplement, or a nutraceutical.

In yet another aspect, the invention is a composition comprising an isoflavonoid suitable for administration as a food stuff, a nutritional supplement, an animal feed supplement, a nutraceutical, or a pharmaceutical, wherein the isoflavonoid is isolated from at least a portion of a transgenic plant transformed with an isolated gene or DNA segment which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, and wherein the transgenic plant exhibits increased levels of an isoflavonoid when compared to the level of the isoflavonoid in plants of the same species which do not comprise the isolated gene or DNA segment.

In yet another aspect, the invention is a method of increasing the nutritional value of a plant by transforming the plant with an isolated gene or DNA segment which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the transgenic plant exhibits increased levels of an isoflavonoid when compared to the level of the isoflavonoid in plants of the same species which do not comprise the isolated gene or DNA segment.

In yet another aspect, the invention is a method of using a transgenic plant transformed with an isolated gene or DNA segment which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the transgenic plant exhibits an increased level of an isoflavonoid when compared to the level of the isoflavonoid in plants of the same species which do not comprise the isolated gene or DNA segment, to provide a nutraceutical benefit to a human or animal administered the isoflavonoid. The isoflavonoid can be administered by ingestion of at least a portion of the plant. The isoflavonoid can also be administered by ingestion of a composition comprising an isoflavonoid isolated from the plant.

In yet another aspect, the invention is a method of using an isoflavonoid isolated from a transgenic plant transformed with an isolated gene or DNA segment which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the transgenic plant exhibits an increased level of an isoflavonoid when compared to the level of the isoflavonoid in plants of the same species which do not comprise the isolated gene or DNA segment, to provide a pharmaceutical benefit to a patient administered the isoflavonoid.

In yet another aspect, the invention is a method of increasing disease resistance in a plant by transforming the plant with an isolated gene or DNA segment which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the transgenic plant exhibits an increased level of an isoflavonoid when compared to the level of the isoflavonoid in plants of the same species which do not comprise the isolated gene or DNA segment.

In yet another aspect, the invention is a method of increasing nodulation efficiency of a leguminous plant by transforming the plant with an isolated gene or DNA segment which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the transgenic plant exhibits an increased level of an isoflavonoid released from the roots when compared to the level of the isoflavonoid released from the roots of plants of the same species which do not comprise the isolated gene or DNA segment.

In yet another aspect, the invention is a transgenic leguminous plant exhibiting increased nodulation efficiency transformed with an isolated gene or DNA segment which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the transgenic plant exhibits an increased level of an isoflavonoid released from the roots when compared to the level of the isoflavonoid released from the roots of plants of the same species which do not comprise the isolated gene or DNA segment.

In yet another aspect, the invention is a method of increasing bacterial or fungal symbiosis in a plant by transforming the plant with an isolated gene or DNA segment which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the transgenic plant exhibits an increased level of an isoflavonoid when compared to the level of the isoflavonoid in plants of the same species which do not comprise the isolated gene or DNA segment.

In yet another aspect, the invention is a transgenic plant exhibiting increased bacterial or fungal symbiosis transformed with an isolated gene or DNA segment which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the transgenic plant exhibits an increased level of an isoflavonoid when compared to the level of the isoflavonoid in plants of the same species which do not comprise the isolated gene or DNA segment.

In yet another aspect, the invention is a transgenic plant comprising at least one recombinant DNA sequence encoding a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the transgenic plant exhibits an increased level of an isoflavonoid when compared to the level of the isoflavonoid in plants of the same species which do not comprise the recombinant DNA sequence.

In yet another aspect, the invention is seed from a transgenic plant comprising at least one recombinant DNA sequence encoding a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the transgenic plant exhibits an increased level of an isoflavonoid when compared to the level of the isoflavonoid in plants of the same species which do not comprise the recombinant DNA sequence.

In yet another aspect, the invention is progeny from a transgenic plant comprising at least one recombinant DNA sequence encoding a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the transgenic plant exhibits an increased level of an isoflavonoid when compared to the level of the isoflavonoid in plants of the same species which do not comprise the recombinant DNA sequence.

In yet another aspect, the invention is progeny from seed of a transgenic plant comprising at least one recombinant DNA sequence encoding a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the transgenic plant exhibits an increased level of an isoflavonoid when compared to the level of the isoflavonoid in plants of the same species which do not comprise the recombinant DNA sequence.

In yet another aspect, the invention is use of a transgenic plant transformed with an isolated gene or DNA segment which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the transgenic plant exhibits an increased level of an isoflavonoid when compared to the level of the isoflavonoid in plants of the same species which do not comprise the isolated gene or DNA segment, for the preparation of a nutraceutical preparation for achieving a nutritional effect.

In yet another aspect, the invention is use of a transgenic plant transformed with an isolated gene or DNA segment which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the transgenic plant exhibits an increased level of an isoflavonoid when compared to the level of the isoflavonoid in plants of the same species which do not comprise the isolated gene or DNA segment, for the preparation of a pharmaceutical preparation for achieving a therapeutic effect.

DETAILED DESCRIPTION

One aspect of the present invention is an isolated gene which encodes the first step of the isoflavone synthase reaction: a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavone. Genes and corresponding cDNA of the soybean or Medicago truncatula CYP93 family have been isolated. The enzymes encoded by the genes of the present invention are isoflavone synthases (IFS) and can catalyze the aryl migration of a flavanone to yield an isoflavone either directly or through the intermediacy of a 2-hydroxyisoflavanone. One isolated soybean gene is classified as CYP93C1v2.

Cytochrome P450 enzymes belong to a large superfamily of enzymes that are abundant in every living organism. The P450 nomenclature committee has determined that each P450 should carry a “CYP” designation and arbitrarily divided the superfamily into families (alphabetical designation), subfamilies (numerical designation) and allelic variants (“v” plus numerical designation) based on amino acid identity of >40%, >55%, and >97%, respectively (Nelson, et al. 1993. “The P450 superfamily update on new sequences, gene mapping, accession numbers, early trivial names of enzymes, and nomenclature,” DNA Cell Biol 12:1). Thus, CYP93C1v2 is a variant of the first described P450 belonging to the third subfamily (C) of the ninety-third P450 family.

Utilizing the procedures presented herein, any plant known to produce isoflavonoids may also serve as sources of suitable DNA, or coding sequences may be synthesized in vitro based on the sequences for the IFS genes of the present invention. CYP93 family members can also be obtained from other plant species by polymerase chain reaction amplification methods known to those skilled in the art, using primer sequences corresponding to regions of nucleotide conservation between CYP93 family members. Furthermore, the genes of the present invention are defined by their catalytic activity: the aryl migration of a flavanone to yield an isoflavone. The gene sequences presented as SEQ ID NO:1 and SEQ ID NO:4 are exemplary, and it is understood that modifications to these genes which do not alter the catalytic activity of its encoded protein fall within the scope of the present invention. While a preferred IFS gene contains the entire open reading frame, portions of or the entire 5′ and 3′ untranslated regions as well as portions of the vector sequence can also be present. With the isolation and functional identification of these isoflavone synthase (IFS) genes that encode the first key step in isoflavone formation, the aryl migration reaction, it is now possible to introduce the isoflavonoid pathway into all plant species, including those that do not naturally possess this pathway.

Another aspect of the present invention is a genetically modified plant which has been transformed with a gene of the present invention. For example, when the CYP93C1v2 gene is transferred into the model plant Arabidopsis thaliana, which does not naturally produce isoflavonoids, the isoflavone genistein accumulates as a series of glycoconjugates (Example 1). This demonstrates that the genes of the present invention can be genetically engineered into plants which do not naturally contain the isoflavonoid pathway, and the transgenic plants can then produce isoflavonoids, resulting in plants with improved disease resistance and/or value added health benefits for humans. In the present invention, unless otherwise stated, as used herein, the term “plant” or “progeny” includes plant parts, plant tissue, plant cells, plant protoplasts, plant cell tissue cultures from which plants can be regenerated, plant calli, plant clumps, explants, plant cells that are intact in plants, or parts of plants, such as embryos, pollen, ovules, flowers, capsules, stems, leaves, seeds, roots, root tips, and the like. Furthermore, the present invention includes the IFS genes expressed in various parts of the plant, e.g., in aerial portions of the plant useful for increasing disease resistance or production of health promoting isoflavonoid nutraceuticals, in seeds useful for increasing levels of isoflavones and their conjugates, or in roots useful for increasing disease resistance or production of nodulation gene inducing isoflavones.

In another aspect, the present invention is a method of improving disease resistance and a transgenic plant with increased disease resistance. By transforming a plant which does not naturally make isoflavones with an IFS gene of the present invention, disease resistance can be genetically engineered into the plant by providing the necessary enzyme to convert its natural flavanones into isoflavonoids. The introduction and subsequent expression of an IFS gene of the present invention into a crop species which naturally possesses the isoflavonoid pathway results in increased levels of the isoflavonoid defense compounds.

In another aspect, the present invention is a method of increasing levels of isoflavonoids that might be beneficial to the establishment of bacterial or fungal symbioses with plants and a transgenic plant with an increased capacity for symbiotic association with bacteria or fungi. Bacterial nodulation can be stimulated in transgenic leguminous plants by expression of an IFS gene of the present invention and decreased by expression of antisense constructs or constructs designed to promote gene silencing that contain an intact IFS gene or segments thereof. Mycorrhizal colonization of leguminous plants can also be increased through the introduction and expression of an IFS gene of the present invention.

In yet another aspect, the present invention is a method of producing isoflavonoid compounds in plants or any other organism to be used in nutraceuticals or pharmaceuticals to confer human or animal health benefits. Edible transgenic plants high in isoflavonoids can be utilized as food for humans and animals. Edible compositions high in isoflavonoids can also be made by incorporation of the transgenic plants or plant materials, or by incorporation of isoflavonoids isolated from the transgenic plants. Compositions useful for administration as a food stuff, a nutritional supplement, an animal feed supplement, a nutraceutical, or a pharmaceutical can be made by incorporation of the transgenic plants or plant materials, or by incorporation of isoflavonoids isolated from the transgenic plants. The nutritional value of a plant can be increased by transforming the plant with an IFS gene of the present invention and, as a result, accumulating high amounts of isoflavonoids in the plant.

The soybean IFS gene of the present invention was isolated and purified according to the detailed procedures outlined in Example 2. The DNA sequence is shown in SEQ ID NO:1 and FIG. 2, and the encoded protein sequence of the isolated soybean CYP93C clone is shown in SEQ ID NO:2 and FIG. 3. For comparison, FIG. 3 also shows the protein sequence alignment between the isolated CYP93C clone (SEQ ID NO:2) and CYP93B1 (SEQ ID NO:3), the licorice licodione synthase.

The DNA and protein sequences of the soybean CYP93C1 open reading frame were deposited in the Genbank data base under accession # AF022462. The deposition was made by Siminszky, Dewey and Corbin, and the sequence described as representing a gene induced in soybean in response to herbicide safeners. However, the function of the gene was not known and there was no understanding that it could be involved in isoflavonoid biosynthesis at the time the deposit was made (Siminszky, B., Corbin, F. T., Ward, E. R., Fleischmann, T. J. and Dewey, R. E., 1999, “Expression of a soybean cytochrome P450 monooxygenase cDNA in yeast and tobacco enhances the metabolism of phenylurea herbicides. ” Proc. Natl. Acad. Sci. USA 96: 1750–1755). The sequence of the clone characterized herein differs from CYP93C1 in three nucleotide substitutions in the open reading frame that change proline 140 to leucine, threonine 156 to isoleucine, and glutamate 295 to lysine. Thus, the soybean gene identified herein has been classified as CYP93C1v2.

The cDNA insert from CYP93C1v2 was used to probe 240,000 phage plaques from a Medicago truncatula root cDNA library (van Buuren, M. L., I. E. Maldonado-Mendoza, A. T. Trieu, L. A. Blaylock, and M. J. Harrison, 1999, “Novel genes induced during an arbuscular mycorrhizal (AM) symbiosis formed between Medicago truncatula and Glomus versiforme,” Mol. Plant-Microbe Interact. 12, 171–181). Five positive plaques were purified, in vivo excised, and sequenced. A full length clone designated mtIFSE3 was completely sequenced on both strands, and shown to encode the Medicago truncatula homolog of soybean CYP93C1. The nucleotide sequence of mtIFSE3 is shown in SEQ ID NO:4 and FIG. 4, and the protein sequence, in SEQ ID NO:5. An alignment between the protein sequences of mtIFSE3 and CYP93C1v2 is shown in FIG. 5.

An IFS gene of the soybean or Medicago truncatula CYP93C subfamily or corresponding cDNA sequence, the open reading frame of which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavone, either directly or through the intermediacy of a 2-hydroxyisoflavanone, can be used to introduce the isoflavonoid pathway into any plant species that does not naturally possess this pathway. Soybean CYP93C1v2 acts on the flavanones liquiritigenin to yield daidzein, and naringenin to yield genistein. Liquiritigenin is only formed in plants that possess the enzyme chalcone reductase (CHR) (Welle, R. and Grisebach, H., 1989, “Phytoalexin synthesis in soybean cells: elicitor induction of reductase involved in biosynthesis of 6′-deoxychalcone. ” Arch Biochem Biophys 272: 97–102), and a form of chalcone isomerase that is active against 2′,4,4′-trihydroxychalcone, the product of the co-action of chalcone synthase (CHS) with CHR (Dixon, R. A., Blyden, E. R., Robbins, M. P., van Tunen, A. J. and Mol, J. N. M., 1988, “Comparative biochemistry of chalcone isomerases.” Phytochemistry 27: 2801–2808). Such genes are common in legumes, but not in most other plant families. Thus, to form daidzein in transgenic plants that do not possess the isoflavonoid pathway, it would be necessary to introduce three new genes, namely CHR, to co-act with CHS to form 2′,4,4′-trihydroxychalcone, a suitable CHI to convert 2′,4,4′-trihydroxychalcone to liquiritigenin, and IFS, assuming that the 2-hydroxyisoflavanone intermediate can spontaneously dehydrate in planta, a phenomenon that is demonstrated below. Without CHR present, no liquiritigenin would be formed, and IFS would only be able to act on naringenin to yield, assuming spontaneous dehydration of the 2-hydroxyisoflavanone, genistein.

The IFS genes of the present invention can be introduced into non-leguminous plants such as by standard Agrobacterium-based or biolistic transformation procedures (Horsch, et al., 1985, “A simple and general method for transferring genes into plants,” Science 227:1229–1231; and Klein, et al., 1988, “Stable genetic transformation of intact Nicotiana cells by the particle bombardment process,” Proc Natl Acad Sci USA 85:8502–8505). Both procedures require the construction of a plasmid vector containing a desirable transcriptional promoter driving expression of the gene of interest (in this case IFS), followed by a transcriptional terminator and a selectable marker gene for resistance, such as to an antibiotic or a herbicide. The biolistic procedure coats metal particles with plasmid DNA containing the gene of interest and places them on a micro carrier disk. Using the biolistic apparatus, the particles are physically propelled into plant tissue. The plant tissue is then put under selection (e.g., antibiotic or herbicide) followed by regeneration. The two Agrobacterium-based procedures are “in planta” and “ex-planta”, respectively. Both procedures require the above gene construct to be placed into a T-DNA vector, which is then transferred into Agrobactrium tumefaciens. The in planta procedure places the transformed Agrobacterium in the presence of plant material (flower or meristem) and the plants are allowed to seed followed by selection (e.g., antibiotic or herbicide) during germination. The ex-planta procedure also places Agrobacterium in the presence of plant material (callus, cell culture, leaf disk, hypocotyl) which is placed directly under selection (e.g., antibiotic or herbicide) followed by regeneration.

Thus, the isoflavonoid pathway can be introduced into any plant species that does not possess the enzyme catalyzing the IFS reaction by expressing the IFS gene in transgenic plants under the control of a suitable constitutive or inducible promoter.

EXAMPLE 1 Transformation of Arabidopsis thailiana with Soybean CYP93C1V2

Soybean CYP93C1v2 cDNA was placed in the binary plant transformation vector pCHF3, in which it is under control of the cauliflower mosaic virus 35S promoter, using standard recombinant DNA methods (Sambrook, et al. 1989. Molecular Cloning. A Laboratory Manual, 2nd Ed, Cold Spring Harbor Laboratory Press, New York). The gene was then transformed into plants of the crucifer, Arabidopsis thaliana ecotype Columbia, using Agrobacterium tumefaciens and a standard floral infiltration procedure (Clough, S. J. and Bent, A. F., 1998, “Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana”. Plant J 16: 735–743). Transgenic plants were selected by germinating the seedlings on kanamycin, and those surviving selection were allowed to set seed. T₂ seedlings expressing CYP93C1v2 were identified by standard DNA and RNA gel blot analysis (Sambrook, et al. 1989. Molecular cloning. A Laboratory Manual, 2nd Ed, Cold Spring Harbor Laboratory Press, New York), and analyzed for accumulation of genistein in leaves by HPLC analysis, according to a method developed to profile the flavonoid components of Arabidopsis leaves (Graham, T. L., 1998, “Flavonoid and flavonol glycoside metabolism in Arabidopsis”. Plant Physiol Biochem 36: 135–144).

FIG. 6A shows a typical HPLC trace of a leaf extract from an untransformed plant. The major components are glycosides (containing glucose and rhamnose) of the flavonols kaempferol and quercetin. Plants harboring the soybean CYP93C1v2 gene showed an additional three peaks on HPLC analysis (FIG. 6B), indicated by the arrows labeled as “1,” “2” and “3.” No free genistein, free 2-hydroxyisoflavanone or 2-hydroxyisoflavanone conjugates were observed. However, following treatment of extracts with almond β-glucosidase (FIG. 7B), one of the new peaks disappeared, and free genistein was now observed, consistent with the peak being a glucoside of genistein. LC-MS analysis confirmed the identities of the new compounds as a glucoside of genistein, glucose-rhamnose-genistein, and rhamnose-genistein (FIGS. 6C and 7C and 7D, insets). Therefore, expression of CYP93C1v2 in transgenic Arabidopsis leads to formation of genistein with no requirement for an enzyme to catalyze the dehydration of the presumed 2-hydroxyisoflavanone intermediate. Arabidopsis plants then modify the genistein by exactly the same chemistry they use to conjugate their endogenous flavonols, namely by conjugation to glucose and rhamnose. Transgenic production of conjugates of genistein are suitable for nutraceutical applications, because genistein is also glycosylated in soybean, its natural dietary source (Graham, T. L., 1991, “Flavonoid and isoflavonoid distribution in developing soybean seedling tissues and in seed and root exudates.” Plant Physiol 95: 594–603).

In addition to introducing the isoflavonoid pathway into plants that do not possess this pathway, the level of isoflavonoid compounds can be controlled in plants that do possess the pathway by manipulating the level of expression of the IFS gene. Increasing the levels of isoflavonoid compounds in leguminous plants by expression of the IFS gene of the present invention in transgenic plants under the control of a suitable constitutive or inducible promoter can be accomplished by standard methods such as Agrobacterium-based or biolistic transformation methods known in the art. Alternatively, the level of isoflavonoid compounds in plants can be reduced by expression of antisense constructs or constructs designed to promote gene silencing that contain an intact IFS gene, or segments thereof, in transgenic plants using methods known in the art. (Bourque, J. E., 1995, “Antisense strategies for genetic manipulations in plants,” Plant Science 105:125–149; and Angell, S. M. and D. C. Baulcombe, 1997, “Consistent gene silencing in transgenic plants expressing a replicating potato virus X RNA,” EMBO J. 16:3675–3684). Antisense constructs for gene silencing are constructed by placing the whole or part of the cDNA in a three prime to five prime orientation behind a desirable transcriptional promoter and ahead of a transcriptional terminator in a plasmid vector. The vector may be used for biolistic transformation or the new antisense gene may be transferred to a T-DNA vector for Agrobacterium-based transformation. The actual mechanism of silencing by antisense constructs is unknown. Homology-dependent gene silencing or co-suppression requires the over-expression of a homologous gene; therefore, to achieve co-suppression a construct is made using a strong promoter, the gene of interest (in this case IFS) and a transcriptional terminator. The gene should be transferred to plants as described above. Gene silencing is an epigenetic phenomenon that may or may not occur with a particular gene construct. When it does occur, the inhibition of gene expression can be greater than with the antisense approach.

Isoflavones can be synthesized from flavanones, utilizing recombinant IFS expressed in any suitable bacterial, fungal, algal, or insect cell system. For example, naringenin is extracted in large amounts from grapefruits. A CYP93C1 enzyme can be used convert naringenin to 2,5,7,4′-tetrahydroxyisoflavanone, which spontaneously converts to the valuable nutraceutical genistein under weak acid conditions. Furthermore, daidzin can be synthesized from liquiritigenin utilizing recombinant CYP93C1 and an isoflavone glucosyltransferase (Köster, J. and W. Barz, 1981, “UDP-Glucose: isoflavone 7-O-glucosyltransferase from roots of chick pea (Cicer arietinum L.).” Arch Biochem Biophys 212: 98–104).

EXAMPLE 2 Methodology Used to Isolate and Identify IFS cDNA Clones

In an attempt to obtain cDNA clones encoding IFS, a functional genomics approach was followed. IFS activity is present in soybean seeds, which accumulate daidzein and genistein. Furthermore, IFS activity can be induced in soybean tissues in response to infection with Phylophthora infestans, associated with the accumulation of the isoflavonoid phytoalexin glyceollin (Bhattacharyya, M. K. and E. W. B. Ward, 1987, “Biosynthesis and metabolism of glyceollin I in soybean hypocotyls following wounding or inoculation with Phytophthora megasperma f. sp. glycinea,” Physiol Mol Plant Path 31: 387–405). It was also known that an enzyme catalyzing a similar reaction to IFS, namely the 2-hydroxylation of flavanone but without aryl migration, belongs to the CYP93B1 subclass of cytochrome P450s (Akashi, et al, 1998, “Identification of a cytochrome P450 cDNA encoding (2S)-flavanone 2-hydroxylase of licorice (Glycyrrhiza echinata L.: Fabaceae) which represents licodione synthase and flavone synthase II,” FEBS Letters 431: 287–290). We therefore searched an expressed sequence tag (EST) database of partial soybean sequences obtained by mass sequencing of two cDNA libraries: a Phytophthora-infected hypocotyl cDNA library (48 hours after infection) and a mid to late developmental stage seed library. Nine candidate P450 sequences were identified, of which three belonged to the CYP93 family. DNA probes were made from the EST clones of the three CYP93 candidates and were used to probe an RNA blot of transcripts from alfalfa suspension cells at various times after exposure to yeast elicitor, a treatment known to induce IFS activity at the onset of isoflavonoid phytoalexin accumulation (Kessmann, et al., 1990, “Stress responses in alfalfa (Medicago sativa L.) III. Induction of medicarpin and cytochrome P450 enzyme activities in elicitor-treated cell suspension cultures and protoplasts,” Plant Cell Reports 9: 38–41). One P450 probe cross-hybridized and detected alfalfa transcripts that were strongly induced by elicitation. This probe was derived from a clone with high homology to soybean CYP93C1 as described below, and the insert in the EST clone was full length. The insert was excised and then cloned into the baculovirus expression system for functional identification by heterologous expression in insect cells (Pauli, H. H. and T. M. Kutchan, 1998, “Molecular cloning and functional heterologous expression of two alleles encoding (S)-N-methylcoclaurine 3′hydroxylase (CYP80B1), a new methyl jasmonate-inducible cytochrome P450-dependent mono-oxygenase of benzylisoquinoline alkaloid biosynthesis,” The Plant J 13: 793–801).

The carbon monoxide difference spectrum of microsomes isolated from insect cells expressing the soybean CYP93C clone indicated the presence of expressed cytochrome P450, as seen from an absorption peak at 450 nm that was not present in similar spectra from insect microsomes originating from cells transformed with a control vector. Unlabeled liquiritigenin was then fed to the microsomes in the presence of NADPH. The substrate remained unconverted in microsomes from cells harboring the control vector. However, in microsomes expressing the CYP93C clone, a new peak of RT 29.96 min was observed by high performance liquid chromatography (FIG. 8A). The amount of this peak was reduced 10-fold if NADPH was omitted from the incubations (FIG. 8B). The UV spectrum of the product, obtained by diode array detection, was identical to that of authentic daidzein (λmax 248 nm, sh 302 nm, λmin 222 nm). The product was collected, derivatized, and analyzed by GC-MS. The mass spectrum of the BSTFA derivative was identical to that of an authentic sample of daidzein (FIG. 9). Microsomes containing the CYP93C clone also metabolized naringenin to yield genistein, although somewhat less efficiently than the reaction with liquiritigenin (FIG. 8C). Insect cell microsomes expressing a different soybean cytochrome P450 cDNA, CYP93E, did not convert liquiritigenin to daidzein when incubated in the presence of NADPH (FIG. 8D). These results indicate that the soybean CYP93C encodes IFS.

EXAMPLE 3 Method of Increasing Dietary Isoflavonoid Intake

Transgenic tomato plants are produced by the introduction of CYP93C1v2 via standard Agrobacterium-based procedures. In a preferred embodiment, the CYP93C1v2 coding sequence is under control of a gene promoter giving specific expression in the fruit. Progeny containing the coding region of the CYP93C1v2 gene are selected at the seedling stage by standard polymerase chain reaction and/or DNA blot analysis known to those skilled in the art. Plants scoring positive for possession of the transgene are grown to fruiting, and fruit analyzed for the presence of isoflavones by the HPLC methods shown in FIG. 7 and FIG. 8 of the present invention. Fruit harvested from the transgenic tomato plants are ingested to increase the dietary intake of isoflavonoids.

It is to be understood that the above description is of preferred exemplary embodiments of the invention and is intended to be illustrative of the invention, but is not to be construed to limit the scope of the invention in any way. Modifications may be made in the structural features of the invention without departing from the scope of the invention.

In summary, isoflavones can now be genetically engineered to provide potential human health benefits of dietary isoflavones and to increase disease resistance in plants. Isoflavones can now be produced in transgenic plants species in which isoflavones do not naturally occur, i.e., in species other than legumes. For example, engineering constitutive production of daidzein and/or genistein or their conjugates into tomato, potato, corn, or other popular components of the human diet, leads to human health benefits, such as reduced cancer risk, reduced incidence of osteoporosis, and treatment for alcoholism. Alternatively, introducing infection-inducible isoflavonoid biosynthesis into non-legumes qualitatively complements these plants' phytoalexin defenses against microbial pathogens, whereas over-expression of the isoflavonoid pathway in legumes quantitatively increases this defense response. Finally, modifying the extent of production of isoflavonoids in legume roots positively impacts nodulation efficiency and therefore plant yield. 

1. A method for introducing into a plant the enzyme catalyzing the aryl migration of a flavanone to form an isoflavanone intermediate or an isoflavone, comprising: introducing a DNA segment encoding said enzyme into said plant to form a transgenic plant, wherein the enzyme comprises more than 97% amino acid identity to the polypeptide encoded by nucleotide 36 to nucleotide 1598 of SEQ ID NO: 1 or nucleotide 92 to nucleotide 1657 of SEQ ID NO:4, wherein said transgenic plant expresses said DNA segment under the control of a suitable constitutive or inducible promoter when said transgenic plant is exposed to conditions which permit expression.
 2. The method of claim 1, wherein the plant comprises chalcone synthase, chalcone reductase, and chalcone isomerase genes that are expressed to form liquiritigenin in said plant to cause in vivo formation of daidzein or a daidzein derivative.
 3. The method of claim 2, wherein said plant is transformed with said chalcone synthase, chalcone reductase, and chalcone isomerase genes.
 4. The method of claim 1 or 2, wherein said plant further comprises downstream genes to metabolize said formed isoflavanone intermediate or isoflavone to biologically active isoflavonoid derivatives or conjugates.
 5. The method of claim 4, wherein said downstream genes encode enzymes selected from the group consisting of isoflavone O-methyltransferase, isoflavone 2′-hydroxylase, isoflavone reductase, and vestitone reductase.
 6. The method of claim 5, wherein said plant further comprises a down-stream gene encoding 4′-O methyltransferase to form biochanin A or a biochanin A derivative.
 7. The method of claim 1, wherein the plant is a naturally isoflavonoid-producing plant, and wherein the plant exhibits increased levels of isoflavonoid compounds from the expression.
 8. The method of claim 7, wherein said isoflavonoid is selected from the group consisting of an isoflavonone intermediate, an isoflavone, an isoflavone derivative, and an isoflavone conjugate.
 9. The method of claim 1, wherein said DNA segment comprises isolated genomic DNA.
 10. The method of claim 1, wherein said DNA segment comprises recombinant cDNA.
 11. The method of claim 1, wherein said DNA segment comprises a soybean CYP93C gene.
 12. The method of claim 11, wherein said DNA sequence comprises the sequence from nucleotide 36 to nucleotide 1598 of SEQ ID NO:
 1. 13. The method of claim 1, said DNA segment is a Medicago truncatula homolog of a CYP93C gene.
 14. The method of claim 13, wherein said DNA sequence comprises the sequence from nucleotide 92 to nucleotide 1657 of SEQ ID NO:
 4. 15. The method of claim 8, wherein said flavanone is liquiritigenin.
 16. The method of claim 8, wherein said flavanone is naringenin.
 17. The method of claim 1, further comprising isolating an isoflavonoid from the transgenic plant and using it to prepare a food.
 18. The method of claim 1, further comprising isolating an isoflavonoid from the transgenic plant and using it to prepare a food stuff, a nutritional supplement, an animal feed supplement, a nutraceutical, or a pharmaceutical.
 19. The method of claim 1, wherein said transgenic plant produces an isoflavonoid which provides a pharmaceutical benefit to a patient.
 20. A tansgenic plant transformed with an isolated gene or DNA segment which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the cytochrome P450 comprises more than 97% amino acid identity to the polypeptide encoded by nucleotide 36 to nucleotide 1598 of SEQ ID NO: 1 or nucleotide 92 to nucleotide 1657 of SEQ ID NO:4, wherein said transgenic plant exhibits increased levels of an isoflavonoid when compared to the level of said isoflavonoid in plants of the same species which do not comprise said isolated gene or DNA segment.
 21. The transgenic plant of claim 20, wherein the level of bacterial or fungal symbiosis is increased.
 22. A method of preparing a nutraceutical composition for achieving a nutritional effect using a transgenic plant transformed with an isolated gene or DNA segment which encodes a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the cytochrome P450 comprises more than 97% amino acid identity to the polypeptide encoded by nucleotide 36 to nucleotide 1598 of SEQ ID NO: 1 or nucleotide 92 to nucleotide 1657 of SEQ ID NO: 4, wherein said transgenic plant exhibits increased levels of an isoflavonoid when compared to the level of said isoflavonoid in plants of the same species which do not comprise said isolated gene or DNA segment said method comprising transforming a plant with said DNA segment and preparing a nutraceutical composition from said transformed plant.
 23. Transformed seed from a transgenic plant comprising at least one recombinant DNA sequence encoding a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the cytochrome P450 comprises more than about 97% amino acid identity to the polypeptide encoded by nucleotide 36 to nucleotide 1598 of SEQ ID NO: 1 or nucleotide 92 to nucleotide 1657 of SEQ ID NO:4, wherein the seed comprises the recombinant DNA sequence, wherein said transgenic plant exhibits an increased level of an isoflavonoid when compared to the level of said isoflavonoid in plants of the same species which do not comprise said recombinant DNA sequence.
 24. Transformed progeny from a transgenic plant comprising at least one recombinant DNA sequence encoding a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the cytochrome P450 comprises more than 97% amino acid identity to the polypeptide encoded by nucleotide 36 to nucleotide 1598 of SEQ ID NO: 1 or nucleotide 92 to nucleotide 1657 of SEQ ID NO:4, wherein the progeny comprises the recombinant DNA sequence, wherein said transgenic plant exhibits an increased level of an isoflavonoid when compared to the level of said isoflavonoid in plants of the same species which do not comprise said recombinant DNA sequence.
 25. Transformed progeny from seed of a transgenic plant comprising at least one recombinant DNA sequence encoding a cytochrome P450 that can catalyze the aryl migration of a flavanone to yield an isoflavanone intermediate or an isoflavone, wherein the cytochrome P450 comprises more than 97% amino acid identity to the polypeptide encoded by nucleotide 36 to nucleotide 1598 of SEQ ID NO: 1 or nucleotide 92 to nucleotide 1657 of SEQ ID NO:4, wherein the progeny comprises the recombinant DNA sequence, wherein said transgenic plant exhibits an increased level of an isoflavonoid when compared to the level of said isoflavonoid in plants of the same species which do not comprise said recombinant DNA sequence. 